everyone knows the mechanics of warfare.
But we, the audience, don't know the mechanics of temporal warfare. Anything becomes possible.
But we do, partially - the first version of spheres, that Archer stopped, was temporal warfare, meant do destroy the federation before its beginning.
Presumably, the federation stopped all such attempts across the timeline, whenever the temporal cold war became hot and changes of the timeline were attempted.
And the builders were defeated at Procyon 5 by conventional warfare - a battle the sphere builders knew is probable they will loose.
But, as said, probability != certainty. Many battles in history were won against the odds; Procyon 5 was not among these (from Daniels' perspective, that is).